cervus_filter filters cervus output results of parentage analysis to produce a list of positions of mismatches between Offspring and Parent. These positions are then checked for coverage and quality and values reported.
Cervus can be run as follows
./cervus_filter -g genotype_file -c cervus_output -s output_from_IonTorrent
and requires the following files:
The genotype file can be created with cervus_parse and is also the input file used for Cervus.
The Cervus output file is that produced by the software Cervus for the analysis of parentage.
The Ion Torrent will produce an XLS file from an ampliseq run to be used here.
cervus_filter will output first a list of Parent and Offspring pairs that have a positive LOD score and 3 or less mismatches according to cervus.
Next, cervus filter will report which Parent/Offspring pair do or don't have mismatches, where those mismatches occur and the coverage and quality of those mismatch positions. E.g.
[Offspring] Animal-49762-0005 == Animal-14675-0001 [Parent]
Mismatch in target 848454 for samplesAnimal-49762-0005 and Animal-14675-0001
Coverage = 1356 and Quality = 344.221 for target 848454 in sample Animal-49762-0005
Coverage = 762 and Quality = 7534.77 for target 848454 in sample Animal-14675-0001
[Offspring] Animal-97685-0003 == Animal-78346-0001 [Parent]
There were no mismatches in samples Animal-97685-0003 and Animal-78346-0001
usage: cervus_filter.v0.1.3.py -c CSV -g GENOTYPE -s ION_TORRENT [-h]
Cervus_filter
Optional Arguments:
-h, --help show this help message and exit
Required Arguments:
-c CSV, --csv CSV Output of Cervus in csv format
-g GENOTYPE, --genotype GENOTYPE
input of Cervus (output of Cervus_parse) in csv format
-s ION_TORRENT, --ion_torrent ION_TORRENT
Output of Ion Torrent in tsv format